The early 2-hole brackets are a few mm taller (as noted elsewhere, I believe in "88 Distinctions") than the 3-hole brackets, to allow for not fitting rubber cushions used (as per orignal) on the 3-hole airbox. (Per "88 Distinctions," #34. 2-hole air box brackets 30 mm, 1-4006 (24 mm 4007-onward))
On 2157, i converted a 3-hole box to 2-hole and modified the 3-hole brackets to 2-hole, using a rubber cushion between brackets and box to make up the difference in height.
The difference in height between early and late brackets, if I recall correctly, is the thickness of the rubber cushion.
Using a modified 3-hole bracket without the cushions makes the air box sit at an angle, because the bracket height is shorter.